Pharyngula

Science magazine has an article today on extracting and sequencing proteins from T. rex bones, and I’m already getting email from people wondering whether this is believable, whether it challenges the stated age of dinosaurs, whether this means we can soon reconstruct dinosaurs from preserved genetic information, and even a few creationists claiming this is proof of a young earth. Short answers: it looks like meticulous and entirely credible work to me, these fossil bones are really 68 million years old, and it represents a special case with limits to how far it can be expanded, so scratch “reassemble dinosaur from fragments” off your to-do list.

First thing I have to mention, though, is that this work is precise quantitative chemistry, not biology, and it’s a bit far from my expertise. The authors are using mass spectrometry of very tiny samples of greatly fragmented proteins to get sequences of short peptides. It’s tricky work, because not only are the proteins in very low concentration, but they are degraded and modified by chemical processes, and they are contaminated with minerals and material from the decay and fossilization processes. The peptides they do get are in extremely low concentration, requiring very precise techniques for analysis.

The data isn’t quite as glamorous or easy to grasp as a great honkin’ big dinosaur bone. They wash out and purify an extremely dilute broth from the fossil, run it through a machine, and produce charts like this one.

i-beb275a97dc5f57c873569adcb1f2f4b-trex_spec.jpg
(click for larger image)

The LC/MS/MS fragmentation pattern from a 68-million-year-old T. rex peptide. (A) The experimental MS/MS spectrum for the T. rex doubly charged hydroxylated tryptic peptide sequence GVQPP(OH)GPQGPR from femur bone extract identified by LC/MS/MS. (B) The synthetic version of the same sequence. All major fragment ions from the experimental spectrum are in very good alignment with ions from the synthetic version, confirming the sequence. This molecular sequencing evidence of protein from a 68-million-year-old fossilized bone demonstrates excellent preservation of the T. rex femur and the high sensitivity of state-of-the-art MS technology.

What it is is a plot of the fragments coming through the mass spec, from which the sequence of that 12-amino-acid peptide can be measured. In this case, they also made a synthetic version of the peptide to show that the pattern of peaks was the same.

The researchers end up with a collection of fragmentary protein sequences, not the whole sequence of the protein, and then they compare those short sequences to a database of protein sequences from extant animals to identify partial matches. Then they ask which organisms have the greatest overall similarity to the selection of short sequences.

The T. rex peptide fragments had the greatest similarity to chicken peptides, but also had differences—some fragments matched up better with newt, fish, or frog sequences. That’s actually a good thing: if there weren’t those differences, there would be a strong suspicion of contamination from modern sources. If, for instance, someone had spilled chicken soup on the sample, we would see overwhelming similarity to chickens but not to newts or frogs (the probability that someone spilled their bowl of newt, frog, and chicken noodle soup is considered very, very low).

I’m persuaded that this T. rex bone contained degraded bits of T. rex protein imbedded in it. There are still some limitations, though. The protein they’re identifying is collagen; 90% of the proteins found in bone are collagen, a relatively simple and conserved molecule, so they’ve started with a highly enriched source 98 million years ago and are washing out a few dilute and broken scraps of the molecules now. It’s an impressive accomplishment, but we aren’t going to be reconstructing muscle anatomy and cell and tissue organization from this, or even getting a good sampling of different gene products for phylogenetic analysis. It’s one protein, and it’s a mess, but it’s really there.

There is promise for the future, though.

As technologies become more refined and protein extraction techniques are optimized, more informative material may be recovered. This holds promise for future work on other fossil material showing similar preservation, but also demonstrates a method for obtaining protein sequences from rare or endangered extant organisms whose genomes have note been sequenced. The MS- and bioinformatics-based approach we have used can be applied not only to obtain sequences from extinct organisms, but also to obtain protein sequences from extant organisms whose genomes have not been sequenced and to discover mutations in diseased tissues such as cancers.

That’s the right perspective, I think: they have a technique that is so good, that they can pluck out a signal even from the highly degraded core of a piece of fossilized bone, there are opportunities for extracting sequences from microsamples of other, less exotic tissues.


Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC (2007) Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry. Science 316(5822): 280-285.

Comments

  1. #1 David Marjanovi?
    April 13, 2007

    But does T-Rex taste like chicken?

    No. T. rex soup tastes like chicken soup. We’re talking about bone collagen after all.

  2. #2 David Marjanovi?
    April 13, 2007

    What? IE6? Don’t tell me IE7 has fewer bugs than IE6. :-o

  3. #3 David Marjanovi?
    April 14, 2007

    What temperatures did the interior of this bone reach while the sediment was being compressed into rock?

    Compressed? It can’t have been compressed much. It’s sandstone — medium-grained, porous sandstone. (The porosity likely contributed to the outstanding preservation.) Apart from the original sand grains, it only contains limestone (as cement).

    Having read both papers (yes, there are two, in the same issue of Science), I have a hard time imagining it’s contamination. Among the things not mentioned yet, antibodies against osteocalcin also react — osteocalcin doesn’t occur outside of bone.

    Most interesting is a paper quoted by the first Science paper:

    R. Avci, M. H. Schweitzer, R. D. Boyd, J. L. Wittmeyer, F. Terán Arce & J. O. Calvo (2005): Preservation of Bone Collagen from the Late Cretaceous Period Studied by Immunological Techniques and Atomic Force Microscopy, Langmuir 21, 3584-3590

    Abstract (italics in the original):

    Late Cretaceous avian bone tissues from Argentina demonstrate exceptional preservation. Skeletal elements are preserved in partial articulation and suspended in three dimensions in a medium-grained sandstone matrix, indicating unusual perimortem taphonomic conditions. Preservation extends to the microstructural and molecular levels. Bone tissues respond to collagenase digestion and histochemical stains. In situ immunohistochemistry localizes binding sites for avian collagen antibodies in fossil tissues. Immunohistochemical studies do not, however, guarantee the preservation of molecular integrity. Aprotein may retain sufficient antigenicity for antibody binding even though degradation may render it incapable of original function. Therefore, we have applied atomic force microscopy to address the integrity and functionality of retained organic structures. Collagen pull-off measurements not only support immunochemical evidence for collagen preservation for antibody recognition but also imply preservation of the whole molecular integrity. No appreciable differences in collagen pull-off properties were measured between fossil and extant bone samples under physiological conditions.

    So they didn’t do this for the first time. I suppose finding out that collagen from a bird “tastes like chicken” wasn’t good enough for Science… even though that bird is older than Tyrannosaurus by something like 10 million years!

    Dump Microsoft.

    That’s much easier said than done. Oh, and, for the record, I don’t use the useless Outlook, I use Outlook Express. If you have a decent (freeware) antivirus program, and if you recognize phishing when you see it, that’s no problem as far as I can see.

    Has the WINE stopped utterly sucking in the last 4 years?

    I would be more concerned with the peptide bonds being broken down just due to time.

    Why should that happen, especially as long as the (porous and well-drained) sandstone stays reasonably dry?